R/normalize.r

In mfmiles/Sscore2: Sscore2: an R package for microarray analysis for Affymetrix/Thermo Fisher arrays

normalize <- function (Score) {
	#x <- unique(Score)
	x <- Score
	Sx <- sum(x)
	Sxx <- sum(x*x)
	Sstdev <- sqrt((Sxx-Sx*Sx/length(Score))/length(Score))
	meanSx <- Sx/length(Score)
	x <- Score-meanSx;
	x <- x[abs(x) < 3*Sstdev]
	Sx <- sum(x)
	Sxx <- sum(x*x)
	num <- length(x)
	Sstdev <- ((Sxx-Sx*Sx/num)/num)
	# Cutoff calculation removed from Sscore 2algorithm
	# if (Sstdev < 0.01) {
	# 	Sstdev <- 1.0
	# } else {
	# 	Sstdev <- sqrt(Sstdev)
	# }
	# readded on 09.27.19:
	Sstdev <- sqrt(Sstdev)
	meanSx <- Sx/num+meanSx
	Score <- (Score-meanSx)/Sstdev
	return(Score)
}